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Yorodumi- EMDB-10318: Complex IV of the III2-IV5B1 respiratory supercomplex from S. cer... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10318 | |||||||||
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Title | Complex IV of the III2-IV5B1 respiratory supercomplex from S. cerevisiae after focused refinement | |||||||||
Map data | None | |||||||||
Sample |
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Function / homology | Function and homology information matrix side of mitochondrial inner membrane / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase ...matrix side of mitochondrial inner membrane / mitochondrial cytochrome c oxidase assembly / protein processing involved in protein targeting to mitochondrion / mitochondrial respiratory chain complex III assembly / Respiratory electron transport / mitochondrial respirasome assembly / Mitochondrial protein degradation / : / : / cytochrome-c oxidase / : / quinol-cytochrome-c reductase / cellular respiration / ubiquinol-cytochrome-c reductase activity / mitochondrial electron transport, cytochrome c to oxygen / cytochrome-c oxidase activity / mitochondrial electron transport, ubiquinol to cytochrome c / mitochondrial crista / electron transport coupled proton transport / ATP synthesis coupled electron transport / enzyme regulator activity / proton transmembrane transport / aerobic respiration / nuclear periphery / mitochondrial membrane / mitochondrial intermembrane space / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / proteolysis / zinc ion binding / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||
Authors | Marechal A / Hartley A / Pinotsis N | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Rcf2 revealed in cryo-EM structures of hypoxic isoforms of mature mitochondrial III-IV supercomplexes. Authors: Andrew M Hartley / Brigitte Meunier / Nikos Pinotsis / Amandine Maréchal / Abstract: The organization of the mitochondrial electron transport chain proteins into supercomplexes (SCs) is now undisputed; however, their assembly process, or the role of differential expression isoforms, ...The organization of the mitochondrial electron transport chain proteins into supercomplexes (SCs) is now undisputed; however, their assembly process, or the role of differential expression isoforms, remain to be determined. In , cytochrome oxidase (CIV) forms SCs of varying stoichiometry with cytochrome (CIII). Recent studies have revealed, in normoxic growth conditions, an interface made exclusively by Cox5A, the only yeast respiratory protein that exists as one of two isoforms depending on oxygen levels. Here we present the cryo-EM structures of the III-IV and III-IV SCs containing the hypoxic isoform Cox5B solved at 3.4 and 2.8 Å, respectively. We show that the change of isoform does not affect SC formation or activity, and that SC stoichiometry is dictated by the level of CIII/CIV biosynthesis. Comparison of the CIV- and CIV-containing SC structures highlighted few differences, found mainly in the region of Cox5. Additional density was revealed in all SCs, independent of the CIV isoform, in a pocket formed by Cox1, Cox3, Cox12, and Cox13, away from the CIII-CIV interface. In the CIV-containing hypoxic SCs, this could be confidently assigned to the hypoxia-induced gene 1 (Hig1) type 2 protein Rcf2. With conserved residues in mammalian Hig1 proteins and Cox3/Cox12/Cox13 orthologs, we propose that Hig1 type 2 proteins are stoichiometric subunits of CIV, at least when within a III-IV SC. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10318.map.gz | 204 MB | EMDB map data format | |
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Header (meta data) | emd-10318-v30.xml emd-10318.xml | 19.6 KB 19.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10318_fsc.xml | 13.4 KB | Display | FSC data file |
Images | emd_10318.png | 79.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10318 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10318 | HTTPS FTP |
-Validation report
Summary document | emd_10318_validation.pdf.gz | 295 KB | Display | EMDB validaton report |
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Full document | emd_10318_full_validation.pdf.gz | 294.1 KB | Display | |
Data in XML | emd_10318_validation.xml.gz | 13.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10318 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10318 | HTTPS FTP |
-Related structure data
Related structure data | 6t15MC 6t0bC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10318.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.048 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Complex IV of the III2-IV(5B)1 respiratory supercomplex from S. c...
+Supramolecule #1: Complex IV of the III2-IV(5B)1 respiratory supercomplex from S. c...
+Macromolecule #1: Cox1 Cytochrome c oxidase subunit 1
+Macromolecule #2: Cox2 Cytochrome c oxidase subunit 2
+Macromolecule #3: Cox3 Cytochrome c oxidase subunit 3
+Macromolecule #4: Cox4 Cytochrome c oxidase subunit 4
+Macromolecule #5: Cox5B Cytochrome c oxidase subunit 5B
+Macromolecule #6: Cox6 Cytochrome c oxidase subunit 6
+Macromolecule #7: Cox7 Cytochrome c oxidase subunit 7
+Macromolecule #8: Cox8 Cytochrome c oxidase polypeptide VIII
+Macromolecule #9: Cox9 Cytochrome c oxidase subunit 7A
+Macromolecule #10: Cox12 Cytochrome c oxidase subunit 6B
+Macromolecule #11: Cox13 Cytochrome c oxidase subunit 6A
+Macromolecule #12: Cox26, Uncharacterized protein YDR119W-A
+Macromolecule #13: RCF2, Respiratory supercomplex factor 2, mitochondrial
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV Details: 3 microliter of sample applied to negatively glow discharged grid, blot force -10; blotting time 8.5 sec.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |